# DeconCell

## Documentation for package ‘DeconCell’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

cell.proportions | Cell Proportion data Example cell proportions of circulating immune cell subpopulations from 5 healthy individuals
count.table | Expression data Example RNA-seq data from 5 healthy individuals
dCell.evaluate | Evaluate percentage of coeficient used in a model 'dCell.predict' Predicts cell proportions of 32 cell subpopulations usin decon Cell models.
dCell.exp.trimming | Trims a dCell.exp matrix for only dCell genes 'dCell.predict' Loads a the gene list used in all dCell models and trims a dCell.exp matrix.
dCell.expProcessing | Pre-process RNASeq based expression data. 'dCell.expProcessing' Performes a TMM normalization, log2(counts+1) and scaling.
dCell.geneList | DeconCell gene list Vector of gene names (ENSEMBL identifiers) used in all of the Decon cell models
dCell.models | DeconCell models Lists fo 33 lists containing the coefficients used in the prediction of cell proportions using expression values
dCell.names | Cell subpopulation names Code and names for the predicted cell subpopulations in the DeconCell package
dCell.predict | Predict all available cell subpopoulation in DeconCell 'dCell.predict' Runs dCell.predict
dCell.predict.single | Predict a single cell subpopoulation using a DeconCell model 'dCell.predict.single' Predicts cell proportions of one out of the 32 cell subpopulations using the DeconCell models.
dCell.run | Run Decon-cell to generate new gene signature and characterize marker genes. 'dCell.run' Runs dCell.run to generate gene expression signatures to predict cell proportions of bulk tissues
dCell.run.single | Run DeconCell to generate new gene signature for a single cell type. 'dCell.run.single' Runs dCell.run to generate gene expression signatures to predict cell proportions of bulk tissues
get.marker.genes | Wrapper function for glmnet 'get.marker.genes'
glmnet.wrapper | Wrapper function for glmnet 'glmnet.wrapper'